BSDB

The conformational change and the identification of the mechanical clamp for proteins can be derived by looking at the unfolding scenario. A unfolding scenario shows distance d_u at which a given native contact is broken for the last time. Contacts in the scenario diagrams are identified by the sequential distance |j - i|. A contact is said to be broken if the distance between amino acids i and j exceeds 1.5σ_ij. An accumulation of many contacts unfolding events at a value of d_u indicates emergence of a force peak. In such figure the y-axis shows the sequential separation between two amino acids that make a native contact. The x-axis indicates at which displacement of the pulling tip the contact is broken for the last time. Notice that thermal fluctuations may reinstate a broken contact temporarily and that’s why we seek the last, and thus definitive, rupture event.

As an example we show the unfolding diagram for the first chain of protein 1c4p. This protein contains an α helix (196-210), denoted as I, and eight β strands, denoted as A through H, as labelled consecutively from the N to C termini. These β strands form three β sheets: a, b, and c. The a sheet comprises four strands (A, B, G, E), b sheet two ( C, F), and c-sheet also two ( D, H). These letters are indicated on the unfolding scenario figure and show which secondary structures are involved in a contact that is broken at the distance d_u. The data symbols marked by asterisks correspond to contacts which do not involve any secondary structures. The remaining symbols are diversified and have a meaning identified by the letter symbols placed next to them. The force peak at about 140 Å involves a near simultaneous rupture of the contacts which relate to the terminal strands A and G: A+G (meaning between A and G), A+I, G+I (i.e. with the helix) as well as D+H, A+B, E+G, D+G, C+G, and A+C. Breaking these contacts results in destroying the a β-sheet. Later on, the remaining contacts, such as C+F in the b sheet are broken and the helix is the last to unravel.

ICN I J |I-J| Displacement error 1 8 40 32 75.97 14.72 2 8 44 36 68.62 11.11 3 8 51 43 31.69 1.21 4 9 12 3 241.15 0.42 5 9 13 4 239.04 0.55 6 9 54 45 31.70 1.21 7 9 58 49 31.54 1.12 8 10 13 3 239.41 0.38 9 10 14 4 242.03 0.04 10 11 14 3 249.43 3.65 11 11 15 4 241.15 0.49 12 11 32 21 131.35 0.90 13 11 33 22 131.16 0.89 14 11 37 26 130.38 0.96 15 12 15 3 240.29 0.83 16 12 16 4 237.75 1.22 17 12 51 39 45.47 0.46 18 12 55 43 43.70 0.02 19 13 16 3 248.75 0.71 20 13 17 4 244.48 2.76 21 14 17 3 248.30 0.93 22 14 18 4 248.30 0.93 23 14 32 18 131.55 0.93 24 14 33 19 131.39 0.92 25 14 37 23 131.31 0.96 26 15 18 3 250.47 0.40 27 15 24 9 137.71 1.50 28 15 29 14 131.59 0.93 29 15 32 17 131.44 0.90 30 15 33 18 131.35 0.92 31 16 19 3 251.02 0.67 32 16 24 8 135.78 1.25 33 16 26 10 134.75 0.73 34 16 29 13 133.31 0.08 35 16 55 39 46.11 0.17 36 16 59 43 45.87 0.12 37 16 61 45 45.97 0.17 38 16 80 64 40.86 0.08 39 18 24 6 146.28 0.29 40 18 29 11 133.44 0.12 41 19 23 4 201.72 6.72 42 19 24 5 146.28 0.29 43 19 80 61 45.72 0.03 44 21 80 59 45.38 0.04 45 21 81 60 45.02 0.06 46 21 82 61 43.83 0.00 47 22 79 57 46.18 0.11 48 22 80 58 45.79 0.04 49 22 81 59 45.45 0.14 50 23 77 54 46.45 0.05 51 23 78 55 46.36 0.09 52 23 79 56 45.81 0.06 53 23 80 57 45.78 0.04 54 24 29 5 236.81 0.75 55 24 77 53 46.41 0.07 56 24 78 54 46.33 0.11 57 24 80 56 45.78 0.04 58 25 28 3 246.34 0.41 59 25 29 4 239.52 2.09 60 25 75 50 46.67 0.06 61 25 76 51 46.59 0.07 62 25 77 52 46.42 0.07 63 26 29 3 239.53 2.09 64 26 30 4 236.83 0.74 65 26 55 29 46.70 0.09 66 26 76 50 46.66 0.07 67 26 78 52 46.40 0.06 68 27 30 3 245.13 0.34 69 27 31 4 236.80 0.84 70 27 74 47 46.73 0.08 71 27 75 48 46.66 0.07 72 27 76 49 46.63 0.06 73 28 31 3 236.81 0.85 74 28 32 4 236.81 0.85 75 29 32 3 246.21 0.13 76 29 33 4 236.43 1.07 77 30 33 3 237.01 0.79 78 30 34 4 236.43 1.07 79 30 48 18 46.84 0.13 80 31 34 3 249.19 1.15 81 31 35 4 237.00 0.78 82 32 35 3 238.19 1.52 83 32 36 4 235.39 0.25 84 33 36 3 244.31 1.02 85 33 37 4 235.41 0.26 86 33 40 7 214.49 1.43 87 33 51 18 46.98 0.13 88 34 37 3 255.37 0.46 89 34 40 6 214.49 1.44 90 34 41 7 187.81 0.74 91 34 45 11 138.25 1.92 92 34 47 13 138.24 1.91 93 37 40 3 237.91 1.23 94 37 41 4 235.56 0.26 95 38 41 3 243.15 1.39 96 38 42 4 232.87 1.08 97 39 42 3 240.23 2.08 98 39 43 4 235.43 0.32 99 40 47 7 167.34 4.62 100 40 51 11 126.73 13.04 101 44 47 3 269.76 2.29 102 47 50 3 237.63 0.86 103 47 51 4 229.94 0.74 104 48 51 3 243.02 0.84 105 48 52 4 238.44 0.93 106 49 52 3 244.83 1.74 107 49 53 4 240.82 0.24 108 50 53 3 245.73 1.29 109 50 54 4 244.81 1.75 110 51 54 3 254.16 2.93 111 51 55 4 242.47 2.90 112 52 55 3 246.67 0.81 113 52 56 4 246.67 0.81 114 52 78 26 87.33 5.97 115 53 56 3 249.87 0.79 116 53 57 4 238.55 1.05 117 54 57 3 246.66 0.81 118 54 58 4 238.54 1.05 119 55 58 3 242.84 1.10 120 55 59 4 238.52 1.05 121 55 61 6 216.76 0.14 122 55 78 23 87.53 5.88 123 56 60 4 205.64 5.37 124 56 61 5 197.47 2.24 125 56 63 7 188.78 6.53 126 56 78 22 87.93 5.91 127 59 80 21 87.33 5.97 128 61 78 17 87.95 5.91 129 61 79 18 87.81 5.87 130 61 80 19 87.12 5.91 131 62 78 16 87.96 5.91 132 62 79 17 87.83 5.86 133 63 77 14 88.03 5.94 134 63 78 15 87.94 5.91 135 63 79 16 87.93 5.91 136 64 67 3 250.83 2.05 137 64 77 13 88.08 5.96 138 66 70 4 248.46 0.28 139 66 73 7 176.80 1.76 140 66 75 9 97.65 1.37 141 66 76 10 88.31 6.02 142 67 70 3 279.79 1.56 143 67 77 10 93.47 3.42 144 70 73 3 245.00 1.53 145 70 74 4 216.62 0.80 146 70 75 5 146.74 1.55 147 71 75 4 225.96 2.20